In Batman Begins you have Ra's Al Ghul, two different versions, Scarecrow, and Falcone. That is three or four major villains depending on how you count it. Not to mention Zsasz running around and the corruption of Gotham in general being villains.
In The Dark Knight you have Joker, Two Face, the last gasp of the mob as the three major villains. Then you have a subplot where Batman has to go to Hong Kong, and the Scarecrow shows back up.
By my count there are at least 3 major and 2 minor villains in those movies.